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SysBioChalmers / RAVEN

The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.
http://sysbiochalmers.github.io/RAVEN/
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Excel I/O problems using MATLAB 2017b and later #55

Closed danieljcook closed 1 year ago

danieljcook commented 6 years ago

Edit: a workaround for this problem is provided, see: https://github.com/SysBioChalmers/RAVEN/issues/55#issuecomment-478980100

Attempting to import an Excel model (.xlsx) using the command "importExcelModel" results in the following error:

Error using importExcelModel (line 140) Java exception occurred: java.lang.NoClassDefFoundError: org/apache/commons/collections4/ListValuedMap

at org.apache.poi.ss.usermodel.WorkbookFactory.create(WorkbookFactory.java:181)

at org.apache.poi.ss.usermodel.WorkbookFactory.create(WorkbookFactory.java:140)

Caused by: java.lang.ClassNotFoundException: org.apache.commons.collections4.ListValuedMap

at java.net.URLClassLoader.findClass(URLClassLoader.java:381)

at java.lang.ClassLoader.loadClass(ClassLoader.java:424)

at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)

at java.lang.ClassLoader.loadClass(ClassLoader.java:357)

... 2 more

There is no problem importing the same model saved as a .xls spreadsheet.

simas232 commented 6 years ago

This is the problem of Matlab 2017b. It is still possible to fix the Excel model export by adding apache-commons-collections jar file to addJavaPaths, but regarding the Excel file export, onlyl xls format works fine.

According to my investigation, there is nothing bad about Excel I/O functions in RAVEN, but rather the problems of apache-poi itself. I even tried to create a small xlsx file with several rows in columns in one sheet, but the generated xlsx file was non-parsable anyway. Apache POI version 4 should be released soon, let's hope that the upcoming version will fix this issue.

simas232 commented 6 years ago

By the way, Matlab 2017b is already bundled with apache-poi, version 3.15. I am not sure, how Matlab prioritizes Java packages, if jar files with identical names are found in multiple directories, though.

tpfau commented 6 years ago

Out of curiosity: Does this only happen on Windows or also on unix?

I recently was annoyed enough to actually code something based on the xlwrite file-exchange submission also using its own bundled POI. https://nl.mathworks.com/matlabcentral/fileexchange/65824-xlread

simas232 commented 6 years ago

The same happens in Unix as well.

tpfau commented 6 years ago

Strange, doesn't seem to happen here... Do you have a file to test that?

simas232 commented 6 years ago

Yes, I do have it. toyModel.xlsx

tpfau commented 6 years ago

I'm on a unix system, and I can't reproduce it... As mentioned I did have issues in the past with xlsread on Matlab thats why I did implement that xlread wrapper, but since changing to xlread that never occured again.

edkerk commented 6 years ago

@tpfau Just to confirm, you are using MATLAB 2017b?

tpfau commented 6 years ago

I might have the culprit: I didn't want static libraries added so I simply changed the code to use dynamic addition. See #76 And yes: Matlab 2017b on a ubuntu linux system (16.04).

edkerk commented 6 years ago

I now also run Matlab 2017b on Windows and I cannot reproduce the error, neither before or after #76.

@danieljcook can you please check whether you still get this error when using the most recent devel branch that has incorporated #76 ?

simas232 commented 6 years ago

@edkerk, are you able to successfully run functions importExcelModel and exportToExcelFormat in 2017b on Windows?

edkerk commented 6 years ago

@simas232 Exactly, works well with both your provided toyModel as well as real models. Just realize that I don't have any additional Matlab Toolboxes installed, perhaps this means that I have some conflicting JAR's missing?

Click to see my javaclasspath

```matlab >> javaclasspath STATIC JAVA PATH C:\Program Files\MATLAB\R2017b\java\patch C:\Program Files\MATLAB\R2017b\java\jarext\ant.jar C:\Program Files\MATLAB\R2017b\java\jarext\ant-launcher.jar C:\Program Files\MATLAB\R2017b\java\jarext\antlr.jar C:\Program Files\MATLAB\R2017b\java\jarext\felix.jar C:\Program Files\MATLAB\R2017b\java\jarext\scr.jar C:\Program Files\MATLAB\R2017b\java\jarext\axis2\activation.jar C:\Program Files\MATLAB\R2017b\java\jarext\axis2\axiom-api.jar C:\Program Files\MATLAB\R2017b\java\jarext\axis2\axiom-impl.jar C:\Program Files\MATLAB\R2017b\java\jarext\axis2\axis2-adb.jar C:\Program Files\MATLAB\R2017b\java\jarext\axis2\axis2-kernel.jar C:\Program Files\MATLAB\R2017b\java\jarext\axis2\axis2-transport-http.jar C:\Program Files\MATLAB\R2017b\java\jarext\axis2\axis2-transport-local.jar C:\Program Files\MATLAB\R2017b\java\jarext\axis2\commons-httpclient.jar C:\Program Files\MATLAB\R2017b\java\jarext\axis2\geronimo-stax-api.jar C:\Program Files\MATLAB\R2017b\java\jarext\axis2\httpcore.jar C:\Program Files\MATLAB\R2017b\java\jarext\axis2\mail.jar C:\Program Files\MATLAB\R2017b\java\jarext\axis2\neethi.jar C:\Program Files\MATLAB\R2017b\java\jarext\axis2\wsdl4j.jar C:\Program Files\MATLAB\R2017b\java\jarext\axis2\wstx-asl.jar C:\Program Files\MATLAB\R2017b\java\jarext\axis2\XmlSchema.jar C:\Program Files\MATLAB\R2017b\java\jarext\batik-anim.jar C:\Program Files\MATLAB\R2017b\java\jarext\batik-extension.jar C:\Program Files\MATLAB\R2017b\java\jarext\batik-dom.jar C:\Program Files\MATLAB\R2017b\java\jarext\batik-transcoder.jar C:\Program Files\MATLAB\R2017b\java\jarext\batik-awt-util.jar C:\Program Files\MATLAB\R2017b\java\jarext\batik-bridge.jar C:\Program Files\MATLAB\R2017b\java\jarext\batik-gvt.jar C:\Program Files\MATLAB\R2017b\java\jarext\batik-css.jar C:\Program Files\MATLAB\R2017b\java\jarext\batik-parser.jar C:\Program Files\MATLAB\R2017b\java\jarext\batik-ext.jar C:\Program Files\MATLAB\R2017b\java\jarext\batik-gui-util.jar C:\Program Files\MATLAB\R2017b\java\jarext\batik-svggen.jar C:\Program Files\MATLAB\R2017b\java\jarext\batik-codec.jar C:\Program Files\MATLAB\R2017b\java\jarext\batik-svg-dom.jar C:\Program Files\MATLAB\R2017b\java\jarext\batik-script.jar C:\Program Files\MATLAB\R2017b\java\jarext\batik-util.jar C:\Program Files\MATLAB\R2017b\java\jarext\batik-swing.jar C:\Program Files\MATLAB\R2017b\java\jarext\batik-xml.jar C:\Program Files\MATLAB\R2017b\java\jarext\bluecove-emu.jar C:\Program Files\MATLAB\R2017b\java\jarext\bluecove.jar C:\Program Files\MATLAB\R2017b\java\jarext\commons-cli.jar C:\Program Files\MATLAB\R2017b\java\jarext\commons-codec.jar C:\Program Files\MATLAB\R2017b\java\jarext\commons-collections-generic.jar C:\Program Files\MATLAB\R2017b\java\jarext\commons-collections.jar C:\Program Files\MATLAB\R2017b\java\jarext\commons-compress.jar C:\Program Files\MATLAB\R2017b\java\jarext\commons-io.jar C:\Program 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Files\MATLAB\R2017b\java\jar\ja_JP\filesystem_adapter_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ja_JP\findfiles_legacy_resources_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ja_JP\fixedpoint_java_util_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ja_JP\install_api_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ja_JP\install_core_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ja_JP\instructionset_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ja_JP\instrument_java_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ja_JP\jit_activation_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ja_JP\license_agreement_dialog_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ja_JP\lmlogin_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ja_JP\matlab_desktop_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ja_JP\matlab_graphics_java_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ja_JP\matlab_graphics_java_widgets_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ja_JP\matlab_java_core_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ja_JP\matlab_java_project_impl_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ja_JP\matlab_java_widgets_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ja_JP\matlab_login_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ja_JP\matlab_sourcecontrol_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ja_JP\mw_java_foundation_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ja_JP\mw_java_help_ui_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ja_JP\mw_java_html_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ja_JP\online_license_management_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ja_JP\pathtool_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ja_JP\path_api_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ja_JP\professional_activation_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ja_JP\rptgen_mlcomp_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ja_JP\shared_cmlink_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ja_JP\shared_controllib_general_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ja_JP\shared_deployment_java_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ja_JP\shared_hwconnectinstaller_common_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ja_JP\shared_install_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ja_JP\shared_rptgen_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ja_JP\shared_supportpkgservices_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ja_JP\slproject_core_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ja_JP\storage\mldrivedesktop_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ja_JP\supportsoftwareinstaller_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ja_JP\supportsoftwarematlabmanagement_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ja_JP\system_editor_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ja_JP\timeseries_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ja_JP\toolboxmanagement_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ja_JP\toolbox_packaging_java_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ja_JP\trialsinstaller_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ja_JP\universal_login_framework_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ja_JP\webintegration_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ja_JP\web_connectivity_res.jar C:\Program Files\MATLAB\R2017b\java\jar\jit_activation.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\activation_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\addons\common_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\addons\import_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\addons\matlab_addons_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\addons\product_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\addons\supportpackage_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\addons\toolbox_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\addons\zip_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\appdesigner\appdesigner_java_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\appmanagement_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\apps_java_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\comparisons_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\comp_utils_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\datatools\variableeditor_web_java_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\dynamic_resource_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\explorer_resources_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\filechooser_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\filesystem_adapter_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\findfiles_legacy_resources_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\install_api_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\install_core_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\instructionset_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\jit_activation_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\license_agreement_dialog_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\lmlogin_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\matlab_desktop_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\matlab_graphics_java_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\matlab_graphics_java_widgets_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\matlab_java_core_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\matlab_java_project_impl_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\matlab_java_widgets_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\matlab_login_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\matlab_sourcecontrol_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\mw_java_foundation_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\mw_java_help_ui_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\mw_java_html_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\online_license_management_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\pathtool_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\path_api_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\professional_activation_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\shared_cmlink_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\shared_deployment_java_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\shared_install_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\shared_supportpkgservices_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\storage\mldrivedesktop_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\supportsoftwareinstaller_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\supportsoftwarematlabmanagement_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\system_editor_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\timeseries_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\toolboxmanagement_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\toolbox_packaging_java_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\trialsinstaller_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\universal_login_framework_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\webintegration_res.jar C:\Program Files\MATLAB\R2017b\java\jar\ko_KR\web_connectivity_res.jar C:\Program Files\MATLAB\R2017b\java\jarext\lais_server_java_api\lais_server_java_api.jar C:\Program Files\MATLAB\R2017b\java\jar\license_agreement_dialog.jar C:\Program Files\MATLAB\R2017b\java\jar\lmlogin.jar C:\Program Files\MATLAB\R2017b\java\jar\matlabinstaller.jar C:\Program Files\MATLAB\R2017b\java\jar\mde.jar C:\Program Files\MATLAB\R2017b\java\jar\addressbar_api.jar C:\Program Files\MATLAB\R2017b\java\jar\hg.jar C:\Program Files\MATLAB\R2017b\java\jar\ide.jar C:\Program Files\MATLAB\R2017b\java\jar\toolbox\matlab\guide.jar C:\Program Files\MATLAB\R2017b\java\jar\page.jar C:\Program Files\MATLAB\R2017b\java\jar\usm.jar C:\Program Files\MATLAB\R2017b\java\jar\matlab.jar C:\Program Files\MATLAB\R2017b\java\jar\jmi.jar C:\Program Files\MATLAB\R2017b\java\jar\services.jar C:\Program Files\MATLAB\R2017b\java\jar\widgets.jar C:\Program Files\MATLAB\R2017b\java\jar\mlservices.jar C:\Program Files\MATLAB\R2017b\java\jar\timer.jar C:\Program Files\MATLAB\R2017b\java\jar\fatalexit.jar C:\Program Files\MATLAB\R2017b\java\jar\mvm.jar C:\Program Files\MATLAB\R2017b\java\jar\project\api.jar C:\Program Files\MATLAB\R2017b\java\jar\project\impl.jar C:\Program Files\MATLAB\R2017b\java\jar\mlwidgets.jar C:\Program Files\MATLAB\R2017b\java\jar\matlab_login.jar C:\Program Files\MATLAB\R2017b\java\jar\sourcecontrol.jar C:\Program Files\MATLAB\R2017b\java\jarext\webservices\mcr_dws_client\mcr_dws_client.jar C:\Program Files\MATLAB\R2017b\java\jar\mladdonpackaging.jar C:\Program Files\MATLAB\R2017b\java\jarext\connector_api\msscommon\msscommon.jar C:\Program Files\MATLAB\R2017b\java\jarext\webservices\mwlic_client\mw-license-server-client.jar C:\Program Files\MATLAB\R2017b\java\jar\util.jar C:\Program Files\MATLAB\R2017b\java\jar\common.jar C:\Program Files\MATLAB\R2017b\java\jar\mwswing.jar C:\Program Files\MATLAB\R2017b\java\jar\beans.jar C:\Program Files\MATLAB\R2017b\java\jar\mwt.jar C:\Program Files\MATLAB\R2017b\java\jar\xml.jar C:\Program Files\MATLAB\R2017b\java\jar\desktop.jar C:\Program Files\MATLAB\R2017b\java\jar\toolstrip.jar C:\Program Files\MATLAB\R2017b\java\jar\org\netbeans.jar C:\Program Files\MATLAB\R2017b\java\jar\org\openide.jar C:\Program Files\MATLAB\R2017b\java\jarext\saxon.jar C:\Program Files\MATLAB\R2017b\java\jarext\helpsearch.jar C:\Program Files\MATLAB\R2017b\java\jar\help\helpui.jar C:\Program Files\MATLAB\R2017b\java\jar\html.jar C:\Program Files\MATLAB\R2017b\java\jarext\search.jar C:\Program Files\MATLAB\R2017b\java\jar\notification_client_util.jar C:\Program Files\MATLAB\R2017b\java\jar\online_license_management.jar C:\Program Files\MATLAB\R2017b\java\jar\pathtool.jar C:\Program Files\MATLAB\R2017b\java\jar\path_api.jar C:\Program Files\MATLAB\R2017b\java\jarext\connector_api\peer_model_api_java\peer_model_java_api.jar C:\Program Files\MATLAB\R2017b\java\jar\product.jar C:\Program Files\MATLAB\R2017b\java\jar\activationclient.jar C:\Program Files\MATLAB\R2017b\java\jar\deactivation.jar C:\Program Files\MATLAB\R2017b\java\jar\vrd.jar C:\Program Files\MATLAB\R2017b\java\jar\publishparser.jar C:\Program Files\MATLAB\R2017b\java\jarext\aps_api\pubsub_api_java\pubsub_api_java.jar C:\Program Files\MATLAB\R2017b\java\jar\resource_core.jar C:\Program Files\MATLAB\R2017b\java\jar\toolbox\rptgenxmlcomp.jar C:\Program Files\MATLAB\R2017b\java\jar\cmlink\api.jar C:\Program Files\MATLAB\R2017b\java\jar\cmlink\util.jar C:\Program Files\MATLAB\R2017b\java\jar\cmlink\implementations\localcm.jar C:\Program Files\MATLAB\R2017b\java\jar\cmlink\implementations\svncore.jar C:\Program Files\MATLAB\R2017b\java\jar\cmlink\implementations\svnintegration.jar C:\Program Files\MATLAB\R2017b\java\jar\cmlink\implementations\svnkitintegration.jar C:\Program Files\MATLAB\R2017b\java\jar\cmlink\implementations\git.jar C:\Program Files\MATLAB\R2017b\java\jar\cmlink\implementations\msscci.jar C:\Program Files\MATLAB\R2017b\java\jar\cmlink\management.jar C:\Program Files\MATLAB\R2017b\java\jar\toolbox\shared\controllib.jar C:\Program Files\MATLAB\R2017b\java\jar\toolbox\control.jar C:\Program Files\MATLAB\R2017b\java\jar\deployment.jar C:\Program Files\MATLAB\R2017b\java\jar\toolbox\shared\hwconnectinstaller\common.jar C:\Program Files\MATLAB\R2017b\java\jar\instutil.jar C:\Program Files\MATLAB\R2017b\java\jar\toolbox\rptgencore.jar C:\Program Files\MATLAB\R2017b\java\jar\toolbox\shared\hwconnectinstaller\util.jar C:\Program Files\MATLAB\R2017b\java\jar\toolbox\testmeas.jar C:\Program Files\MATLAB\R2017b\java\jar\toolbox\slproject.jar C:\Program Files\MATLAB\R2017b\java\jarext\webservices\ssi_dws_client\ssi_dws_client.jar C:\Program Files\MATLAB\R2017b\java\jar\storage\gdsinmatlab.jar C:\Program Files\MATLAB\R2017b\java\jar\storage\gds.jar C:\Program Files\MATLAB\R2017b\java\jar\storage\provider.jar C:\Program Files\MATLAB\R2017b\java\jar\storage\matlabdrivedesktop.jar C:\Program Files\MATLAB\R2017b\java\jar\storage\motw.jar C:\Program Files\MATLAB\R2017b\java\jar\storage\filesystemadapter.jar C:\Program Files\MATLAB\R2017b\java\jar\supportsoftwareclient.jar C:\Program Files\MATLAB\R2017b\java\jar\supportsoftwareinstaller.jar C:\Program Files\MATLAB\R2017b\java\jar\supportsoftwarematlabmanagement.jar C:\Program Files\MATLAB\R2017b\java\jar\system\editor.jar C:\Program Files\MATLAB\R2017b\java\jar\toolbox\timeseries.jar C:\Program Files\MATLAB\R2017b\java\jar\toolboxmanagement.jar C:\Program Files\MATLAB\R2017b\java\jar\toolbox_packaging.jar C:\Program Files\MATLAB\R2017b\java\jar\trialsinstaller.jar C:\Program Files\MATLAB\R2017b\java\jarext\webservices\udc_client\udc_client.jar C:\Program Files\MATLAB\R2017b\java\jarext\webservices\udc_client_ssi\udc_client_ssi.jar C:\Program Files\MATLAB\R2017b\java\jar\login.jar C:\Program Files\MATLAB\R2017b\java\jarext\webservices\urlmanager\urlmanager.jar C:\Program Files\MATLAB\R2017b\java\jar\webintegration.jar C:\Program Files\MATLAB\R2017b\java\jar\mlwebservices.jar C:\Program Files\MATLAB\R2017b\java\jar\net.jar C:\Program Files\MATLAB\R2017b\java\jar\webproxy.jar C:\Program Files\MATLAB\R2017b\java\jarext\dws_client.jar C:\Program Files\MATLAB\R2017b\java\jarext\webservices\loginws_client.jar C:\Program Files\MATLAB\R2017b\java\jarext\webservices\service_request_client.jar C:\Program Files\MATLAB\R2017b\java\jarext\webservices\dws_client.jar C:\Program Files\MATLAB\R2017b\java\jarext\webservices\ws_client_core\mw-service-client-core.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\activation_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\addons\common_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\addons\import_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\addons\matlab_addons_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\addons\product_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\addons\supportpackage_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\addons\toolbox_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\addons\zip_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\appdesigner\appdesigner_java_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\appmanagement_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\apps_java_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\comparisons_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\comp_utils_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\datatools\variableeditor_web_java_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\dynamic_resource_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\explorer_resources_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\filechooser_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\filesystem_adapter_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\findfiles_legacy_resources_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\install_api_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\install_core_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\instructionset_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\jit_activation_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\license_agreement_dialog_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\lmlogin_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\matlab_desktop_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\matlab_graphics_java_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\matlab_graphics_java_widgets_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\matlab_java_core_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\matlab_java_project_impl_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\matlab_java_widgets_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\matlab_login_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\matlab_sourcecontrol_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\mw_java_foundation_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\mw_java_help_ui_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\mw_java_html_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\online_license_management_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\pathtool_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\path_api_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\professional_activation_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\shared_cmlink_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\shared_deployment_java_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\shared_install_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\shared_supportpkgservices_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\storage\mldrivedesktop_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\supportsoftwareinstaller_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\supportsoftwarematlabmanagement_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\system_editor_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\timeseries_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\toolboxmanagement_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\toolbox_packaging_java_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\trialsinstaller_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\universal_login_framework_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\webintegration_res.jar C:\Program Files\MATLAB\R2017b\java\jar\zh_CN\web_connectivity_res.jar DYNAMIC JAVA PATH C:\Work\GitHub\RAVEN\software\apache-poi\stax-api-1.0.1.jar C:\Work\GitHub\RAVEN\software\apache-poi\xmlbeans-2.3.0.jar C:\Work\GitHub\RAVEN\software\apache-poi\poi-ooxml-schemas-3.8-20120326.jar C:\Work\GitHub\RAVEN\software\apache-poi\poi-ooxml-3.8-20120326.jar C:\Work\GitHub\RAVEN\software\apache-poi\poi-3.8-20120326.jar C:\Work\GitHub\RAVEN\software\apache-poi\dom4j-1.6.1.jar ```

simas232 commented 6 years ago

@edkerk, I think that is the case. Regarding the Matlab installations provided by Chalmers Managed Software Centre, 2017b contains about 20 additional toolboxes not found in 2016b, so one of them likely contributes to the conflicting Java classes. The installation of Matlab is entirely automatic, so I could not choose which toolboxes shall be installed. It is not possible to uninstall these toolboxes via Home -> Add-Ons as well due to the denied access.

Someone has to test whether Excel I/O works fine in the bare Matlab 2017b for macOS. I can do such a test in the following weeks.

simas232 commented 6 years ago

WORKAROUND: Problem solved! The Excel I/O does not work for users who have Text Analytics Toolbox installed. This toolbox uses Apache POI for MS Word docx files parsing and somehow introduces conflicts in Java classes.

The users therefore must remove this toolbox before using RAVEN:

edkerk commented 6 years ago

The problem is in MATLAB\R2017b\java\jarext\tika-app.jar containing conflicting Java libraries. The Apache POI libraries provided by RAVEN are version 3.8, while the MATLAB provided are of version 3.17.

Between these versions, there have been new dependencies (xmlbeans-2.6.0, commons-collections4-4.1) and some code changes that break backwards compatibility. I've been able to trace this back to POI version 3.11-BETA1, but I'm currently stuck in finding changes in subsequent versions (3.11-BETA1 works, but 3.11-BETA2 doesn't...).

simas232 commented 6 years ago

Could be. I was able to trace back Apache POI version 3.15 by looking to the sizes of jar files.

It is not necessary to update Apache POI bundled in RAVEN right now, though. Couple of months ago I tried to run Apache POI 3.17 in MATLAB 2016b, but got other types of errors there, so maybe we should update it only when it is really necessary.

simas232 commented 6 years ago

Maybe I didn't stress it enough, but it is not possible to use Apache POI, bundled with MATLAB thereby ignoring the jar files bundled in RAVEN. I was getting other type of error there.

edkerk commented 6 years ago

While removing Text Analysis Toolbox is a workaround, this is not a solution for users without sufficients rights on their computer (e.g. students on university computers). So it would be prefered to have this work out-of-the-box.

Replacing libraries with 3.17 in commit 07e57550097c4d1921ce68bcbb94144da8f71962 actually writes an XLSX file, but when opening it with Excel it is corrupted. Open and repair works, so all information is there.

Running 07e57550097c4d1921ce68bcbb94144da8f71962 with Matlab 2017b + Text Analysis Toolbox gives an error No constructor 'org.apache.poi.xssf.usermodel.XSSFWorkbook' with matching signature found.. This toolbox comes with Apache Tika 1.14, which is bundled with Apache POI 3.15.

tpfau commented 6 years ago

I have tried to look a bit more into this issue (as its the same with the COBRA toolbox): It seems as if the tika-app.jar shipped by matlab is broken/incomplete (~30Mb while the version from apache is ~50Mb), and probably lacks some dependencies. However, I have not found a way (besides replacing the jar) to get a working POI version while the Text-Analysis toolbox was installed.

laurentheirendt commented 5 years ago

Just reporting that this is the same issue for MATLAB R2018b.

jonovik commented 5 years ago

In recent Matlab, here's how to uninstall the Text Analytics toolbox:

Matlab > HOME toolbar > ENVIRONMENT section > Add-Ons > Manage Add-Ons > search for "text analytics" > button with vertical triple-dot > Uninstall.

After this, the following works on my R2018a:

>> cd path/to/RAVEN
>> smallModel=importExcelModel('empty.xlsx')
smallModel = 
  struct with fields:
                     id: 'empty'
            description: 'Empty model structure'
             annotation: [1×1 struct]
                   rxns: {'r1'}
                       ...
haowang-bioinfo commented 4 years ago

I previously had this problem while using MATLAB (R2018b and R2019b) on my computer (MacOS). Now this bug had been fixed in the latest version (2020).

simas232 commented 4 years ago

@Hao-Chalmers, do you mean that you did not need to remove Text Analytics Toolbox?

haowang-bioinfo commented 4 years ago

@simas232 in my case, no need to do anything under R2020a.

simas232 commented 4 years ago

I ran checkInstallation in MATLAB R2020a (macOS Catalina) with Text Analytics Toolbox installed. Just like before, Excel I/O feature in RAVEN is still incompatible with Text Analytics Toolbox, which must be uninstalled to restore Excel I/O functionality.

siusenphang commented 3 years ago

I'm having the same problem with a twist. In my case the Matlab R2020b run time environment is the one introducing the Java libraries that generate the conflict. My application runs fine in Matlab interactive mode but for execution in a production environment (Linux) we compile our Matlab code with the mcc compiler and use the Matlab run time environment to run it.

My installation of the run time environment comes with a bunch of extra toolboxes I don't need and don't even have a license for, TextAnalytcis is one of them.

As a workaround to have my application working after it is compiled I had to delete a couple of jar files from the run time environment location (see below). I've reached out to Mathworks support to ask if there's an official procedure to select the toolboxes I want to have in the run time environment, the support case is still open. I'm hoping there's a cleaner way to do this.

JAR files removed:

/java/jar/toolbox/textanalytics.jar /java/jarext/tika-app.jar
mihai-sysbio commented 1 year ago

It's been almost 2 years since this issue has been talked about. So, I'm wondering if it's still needed to resolve this (i.e. fixing the export to Excel, if it's even still a problem). My suggestion would be to consider closing the issue and declare this piece of functionality "unmaintained", since it's anyway preferred to use other non-binary file formats.

edkerk commented 1 year ago

It will not be solved. It was remained open and pinned to make it easily findable for people running into this issue. I have since learned how to check if Text Analytics Toolbox is installed. A check for this can be implemented in checkInstallation, which will then provide the necessary instructions. Then, this Issue can be closed and unpinned.

ericamanga commented 1 year ago

Hello, I saw this error, but couldn't fix it. I can not uninstalling the Text Analytics Toolbox. Even though I had this recommendation with checkInstallation.

checkInstallation

THE RAVEN TOOLBOX

Installing from location C:\Users\Usuario\Desktop\bkp\Documents\RAVEN-2.8.0 Checking RAVEN release 2.8.0 You are running the latest RAVEN release Checking MATLAB release 2023a Checking system architecture win64 Set RAVEN in MATLAB path Pass Save MATLAB path Pass

=== Model import and export ===

Add Java paths for Excel format Pass Checking libSBML version 5.19.0 Checking model import and export Import Excel format Fail Export Excel format Fail Import SBML format Pass Export SBML format Pass MATLAB Text Analytics Toolbox found. This should be uninstalled if you want to read/write Excel files. See RAVEN GitHub Issues page for instructions. [...]

But when I go to Manage Add-Ons, I have this error:

Error using matlab.internal.cef.webwindow/errorOnInValidWindow Webwindow is not valid. It was closed by user or the process was terminated.

Error in matlab.internal.cef.webwindow/bringToFront (line 673) obj.errorOnInValidWindow()

Error in matlab.internal.webwindow/bringToFront (line 225) bringToFront(obj.impl)

Error in matlab.internal.addons.AddOnsWindow/bringToFront (line 72) obj.webwindow.bringToFront();

Error in matlab.internal.addons.Manager/show (line 59) obj.addOnsWindowInstance.bringToFront();

Error in matlab.internal.addons.launchers.showManager (line 93) managementUIInstance.show(navigationData);

I know it seems to be more a Matlab error, instead of a RAVEN one, but I would appreciate your support!

Best,

edkerk commented 1 year ago

@ericamanga, this is indeed a Matlab error, but perhaps one of the three following approaches work. I have to admit that only the third one works on my computer, but the other two approaches are taken from Matlab documentation, so they should work, maybe it will for you:

  1. Run matlab.addons.uninstall("Text Analytics Toolbox")
  2. Run TA = struct2table(matlab.addons.toolbox.installedToolboxes); TA = TA(find(strcmp(TA.Name,"Text Analytics Toolbox"))); matlab.addons.toolbox.uninstall(TA);
  3. In Windows, go to Settings --> Apps --> Apps & Features (might be somewhat different dependent on your exact Windows version and language). There, find MATLAB among the list of installed software, click on Uninstall, once again, and confirm that you want to run the uninstaller. Then, you will get a window where you can select all MATLAB components you want to uninstall. Unselect all, except for Text Analytics Toolbox. Click on Uninstall to proceed.

Please let me know if method 1 or 2 perhaps worked on your computer.

edkerk commented 1 year ago

Error message in release 2.8.2 is now informative enough (and links to this Issue), so while not solved this Issue can be closed.